Sodium in PDB 6jy4: Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State

All present enzymatic activity of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State:
1.9.3.1;

The structure of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 6jy4 was solved by K.Shinzawa-Itoh, K.Muramoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	149.395, 152.395, 174.040, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 20.5

The structure of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Zinc	(Zn)	1 atom
Iron	(Fe)	2 atoms
Copper	(Cu)	3 atoms

The binding sites of Sodium atom in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State (pdb code 6jy4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 6jy4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:40.5 occ:1.00 O A:GLY45 2.3 46.3 1.0 O A:GLU40 2.3 40.7 1.0 OE1 A:GLU40 2.3 41.2 1.0 O A:SER441 2.3 38.4 1.0 O A:HOH793 2.3 38.0 1.0 CD A:GLU40 3.2 39.4 1.0 C A:GLU40 3.4 33.4 1.0 O A:HOH782 3.4 46.5 1.0 C A:GLY45 3.4 47.5 1.0 CG A:GLU40 3.5 38.6 1.0 C A:SER441 3.5 35.9 1.0 O A:HOH863 3.7 57.6 1.0 CA A:ASP442 4.0 34.0 1.0 CB A:ASP442 4.0 37.0 1.0 CA A:THR46 4.0 57.1 1.0 O A:GLN43 4.1 41.9 1.0 OD1 A:ASP442 4.1 43.9 1.0 CG A:ASP442 4.1 43.2 1.0 N A:ASP442 4.1 34.7 1.0 N A:THR46 4.2 48.2 1.0 N A:LEU41 4.2 37.7 1.0 CA A:GLU40 4.3 35.4 1.0 CA A:LEU41 4.3 37.4 1.0 OE2 A:GLU40 4.4 45.4 1.0 N A:LEU47 4.4 48.8 1.0 N A:GLY45 4.4 44.6 1.0 CB A:GLU40 4.5 37.0 1.0 CA A:GLY45 4.5 37.6 1.0 C A:THR46 4.7 57.6 1.0 CA A:SER441 4.7 37.1 1.0 CD2 A:LEU41 4.8 35.2 1.0 OD2 A:ASP442 4.8 41.3 1.0 CB A:SER441 5.0 37.0 1.0

Sodium binding site 2 out of 2 in the Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Monomeric Form of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:42.6 occ:0.30 NE2 C:HIS232 2.1 49.8 1.0 NE2 C:HIS148 2.2 56.0 1.0 OE1 C:GLU236 2.3 65.3 1.0 CD C:GLU236 2.9 53.2 1.0 CD2 C:HIS232 2.9 43.6 1.0 CE1 C:HIS148 3.1 57.2 1.0 CD2 C:HIS148 3.2 52.7 1.0 CG C:GLU236 3.3 52.3 1.0 CE1 C:HIS232 3.3 45.5 1.0 OE2 C:GLU236 3.7 46.9 1.0 SD C:MET152 4.1 68.1 1.0 CG C:HIS232 4.2 39.5 1.0 CG C:MET152 4.2 52.1 1.0 ND1 C:HIS148 4.2 61.1 1.0 ND1 C:HIS232 4.3 41.9 1.0 CG C:HIS148 4.3 43.0 1.0 O C:HOH401 4.6 59.0 1.0 CB C:GLU236 4.8 46.6 1.0 O C:HOH402 4.8 45.1 1.0

K.Shinzawa-Itoh, T.Sugimura, T.Misaki, Y.Tadehara, S.Yamamoto, M.Hanada, N.Yano, T.Nakagawa, S.Uene, T.Yamada, H.Aoyama, E.Yamashita, T.Tsukihara, S.Yoshikawa, K.Muramoto. Monomeric Structure of An Active Form of Bovine Cytochromecoxidase. Proc.Natl.Acad.Sci.Usa V. 116 19945 2019.
ISSN: ESSN 1091-6490
PubMed: 31533957
DOI: 10.1073/PNAS.1907183116